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PubMed1997

Molecular diagnostics of infectious diseases.

Over the past several years, the development and application of molecular diagnostic techniques has initiated a revolution in the diagnosis and monitoring of infectious diseases. Microbial phenotypic characteristics, such as protein, bacteriophage, and chromatographic profiles, as well as biotyping and susceptibility testing, are used in most routine laboratories for identification and differentiation. Nucleic acid techniques, such as plasmid profiling, various methods for generating restriction fragment length polymorphisms, and the polymerase chain reaction (PCR), are making increasing inroads into clinical laboratories. PCR-based systems to detect the etiologic agents of disease directly from clinical samples, without the need for culture, have been useful in rapid detection of unculturable or fastidious microorganisms. Additionally, sequence analysis of amplified microbial DNA allows for identification and better characterization of the pathogen. Subspecies variation, identified by various techniques, has been shown to be important in the prognosis of certain diseases. Other important advances include the determination of viral load and the direct detection of genes or gene mutations responsible for drug resistance. Increased use of automation and user-friendly software makes these technologies more widely available. In all, the detection of infectious agents at the nucleic acid level represents a true synthesis of clinical chemistry and clinical microbiology techniques.

Animals↗

PubMed2001

Screening method for identification of beta-lactams in bovine urine by use of liquid chromatography and a microbial inhibition test.

OBJECTIVE: To develop a multiple-residue screening method for the detection of beta-lactams in bovine urine. ANIMALS: 6 clinically normal Holstein cows and 6 calves. PROCEDURE: Pooled urine obtained from cows was used as a negative-control sample or spiked with varying concentrations of 6 beta-lactam antibiotics. Urine samples were prepared for liquid chromatography by diluting 1 ml of urine with 9 ml of 0.01M KH2PO4, 0.01 M Na2PO4, and filtering. Filtrate (2,000 ml) was eluted with a mobile phase in a gradient program. A fraction corresponding to each beta-lactam of interest was collected and evaporated to < 1 ml, and water then was added to achieve a 1 ml volume. The collected fraction was tested, using a microbial inhibition test. Then, calves were fed milk spiked with a mixture of 5 beta-lactam antibiotics at a concentration 40X the FDA tolerance in milk. Three hours following the feeding, urine samples were obtained from the calves and tested, as described for the urine samples for the cows. RESULTS: The lowest concentrations of amoxicillin, ampicillin, cephapirin, cloxacillin, desfuroylceftiofurcysteine, and penicillin G that were consistently detected in urine were 100, 10, 100, 250, 1,000, and 10 ng/ml, respectively. Amoxicillin, ampicillin, cephapirin, cloxacillin, desacetylcephapirin, and penicillin G were detected in urine samples of 6/6, 5/6, 0/6, 6/6, 2/6, and 3/6 calves respectively, fed antibiotic-spiked milk. CONCLUSIONS AND CLINICAL RELEVANCE: The integrated method described can be used to detect or identify beta-lactam antibiotics in bovine urine. This method can be used to test cattle for beta-lactam residues.

Animals↗

PubMed1995

An amperometric opiate assay.

Current techniques for the detection and measurement of diacetylmorphine (heroin), morphine and their principal metabolite morphine-3-glucuronide (M3G) are based mainly on chromatography or immunoassay. No enzymatic method for the detection of these compounds has yet been reported. Two novel microbial enzymes have been isolated and characterized in this laboratory: an acetylmorphine carboxyesterase (heroin esterase) and a morphine dehydrogenase (MDH). These highly specific enzymes have been incorporated in an amperometric assay for heroin and morphine using phenazine methosulphate as a mediator. The assay gives a rapid and sensitive response to heroin and morphine, with a detection limit for morphine of 6.8 micrograms ml-1 (23.7 microM).

Acetylesterase↗

PubMed2005

Real-time microbe detection based on director distortions around growing immune complexes in lyotropic chromonic liquid crystals.

We describe director distortions in the nematic liquid crystal (LC) caused by a spherical particle with tangential surface orientation of the director and show that light transmittance through the distorted region is a steep function of the particle's size. The effect allows us to propose a real-time microbial sensor based on a nontoxic lyotropic chromonic LC (LCLC) that detects and amplifies the presence of immune complexes. A cassette is filled with LCLC, antibody, and antigen-bearing particles. Small and isolated particles cause no macroscopic distortions of the LCLC. Upon antibody-antigen binding, the growing immune complexes distort the director and cause detectable optical transmittance between crossed polarizers.

Antigen-Antibody Complex↗

PubMed1996

Rapid detection and isolation of DNA-binding compounds from Streptomyces xanthochromogenes.

The culture medium of Streptomyces xanthochromogenes JH903 was found to show selective activity against DNA-repair-deficient Escherichia coli CM871 strain. In this report we describe a simple method to locate and isolate DNA binding compounds from the fermentation broth. The method is based on the retention of DNA-reacting compounds in cellulose complexed with DNA, and purification of these compounds with thin-layer chromatography. Screening of microbial metabolites from chloroform extracts of fermentation media resulted in detection of five genotoxic fractions.

DNA↗

PubMed2006

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

BACKGROUND: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. RESULTS: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV) as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication). CONCLUSION: PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.

Computational Biology↗

PubMed1992

Induction of prophage lambda by chlorinated organics: detection of some single-species/single-site carcinogens.

Twenty-eight chlorinated organic compounds were evaluated for their ability to induce DNA damage using the Microscreen prophage-induction assay in Escherichia coli. Comparison of the performance characteristics of the prophage-induction and Salmonella assays to rodent carcinogenicity assays showed that the prophage-induction assay had a somewhat higher specificity than did the Salmonella assay (70% vs. 50%); sensitivity, concordance, and positive and negative predictivity were similar for the two microbial assays. The Microscreen prophage-induction assay failed to detect eight carcinogens, perhaps due to toxicity or other unknown factors; five of these eight carcinogens were detected by the Salmonella assay. However, the prophage-induction assay did detect six carcinogens that were not detected by the Salmonella assay, and five of these were single-species, single-site carcinogens, mostly mouse liver carcinogens. Some of these carcinogens, such as the chloroethanes, produce free radicals, which may be the basis for their carcinogenicity and ability to induce prophage. The prophage-induction (or other SOS) assay may be useful in identifying some genotoxic chlorinated carcinogens that induce DNA damage that does not revert the standard Salmonella tester strains.

Animals↗

PubMed2007

Microbial fuel cell-based biosensor for fast analysis of biodegradable organic matter.

The current study was made to develop a biosensor based on a single-chamber microbial fuel cell in which anaerobes were retained in the anode compartment separated from the cathode compartment by a proton exchange membrane. In the sensor a replaceable anaerobic consortium was used for analyzing biodegradable organic matter. The anaerobes acted as biocatalysts in oxidizing organic matter and transferring electrons to the anode. The biocatalysts were renewed for each sample analysis by replacing the old anaerobic consortium with an equal amount of fresh one. A glucose standard solution was used as the target substrate. To obtain the maximum sensor output, the MFC-based sensor system was optimized using an 800 Omega resistor as the load to the external electric circuit and 25 mM phosphate buffer with 50mM NaCl as catholyte in the aerobic compartment. The temperature of anaerobic compartment was maintained at optimal 37 degrees C. The cell potential across the electrodes increased with increasing loading of glucose. The sensor response was linear against concentration of glucose up to 25 gl(-1). The detection limit was found as 0.025 gl(-1). The microbial fuel cell with replaceable anaerobic consortium could be used as a biosensor for on-line monitoring of organic matter.

Bacteria↗

PubMed2005

Green fluorescent protein for detection of the probiotic microorganism Escherichia coli strain Nissle 1917 (EcN) in vivo.

Probiotic microorganisms are defined as viable nutritional agents conferring benefit to the health of the human host. Especially, Escherichia coli strain Nissle 1917 (EcN) was shown to be equally effective as mesalazine in the maintenance of remission in ulcerative colitis (UC). Presumably, the therapeutic effect of EcN is linked to the presence of the strain in the region of interest; however, it remains difficult to follow the orally administered strain on its passage through the complex microbial environment of the intestine in vivo, inhabited dominantly by various E. coli strains, using traditional culturing methods. In this study we transformed EcN and a wild-type E. coli from a laboratory rat (EcR) with a plasmid carrying a gfp gene (pUC-gfp) to obtain EcN- and EcR-GFP to allow in vivo detection without alteration of strain-specific characteristics. Analysis of different strain-specific characteristics included the measurement of stimulation of IL-8 secretion and adhesion in vitro using the epithelial cell line HT-29. The kinetics of intestinal distribution in mice and colonization properties in rats following oral administration was studied in vivo. Detectability of the strain in histologic specimens was analysed using fluorescence microscopy and immunohistochemistry. The identity of fluorescent E. coli strains isolated from stool samples, Peyer's patches (PP) and mesenteric lymph nodes (MLN) was determined by REP-PCR. We were able to demonstrate that EcN and EcN-GFP do not differ in stimulation of IL-8 secretion or adhesion to HT-29 cells. In vivo, EcN-GFP colonies were readily detectable by fluorescence microscopy in luminal samples and also by immunohistochemistry in histological sections allowing analysis of the kinetics of the intestinal passage following oral administration. Translocation of fluorescent and non-fluorescent bacteria into PP and MLN was noted at 6 h post oral administration. EcN-GFP was detectable initially for 14 days in faecal samples of rats, while EcR-GFP was detectable throughout the whole experiment (45 days). Challenge with ampicillin at day 45 demonstrated continuing presence of EcN-GFP in small numbers by reappearing fluorescent colonies. The plasmid was not stable in vivo since non-fluorescent EcN colonies were detected also in faecal samples by REP-PCR. In summary, transformation of EcN to obtain EcN-GFP in our study had no detectable influence on the probiotic microorganism regarding adhesion on and induction of IL-8 secretion of HT-29 cells and allows the detection in mixed microbial environments in vivo but the stability of EcN-GFP in vivo is limited.

Ampicillin↗

PubMed1998

Microbiology of spent nuclear fuel storage basins.

Microbiological studies of spent nuclear fuel storage basins at Savannah River Site (SRS) were performed as a preliminary step to elucidate the potential for microbial-influenced corrosion (MIC) in these facilities. Total direct counts and culturable counts performed during a 2-year period indicated microbial densities of 10(4) to 10(7) cells/ml in water samples and on submerged metal coupons collected from these basins. Bacterial communities present in the basin transformed between 15% and 89% of the compounds present in Biologtrade mark plates. Additionally, the presence of several biocorrosion-relevant microbial groups (i.e., sulfate-reducing bacteria and acid-producing bacteria) was detected with commercially available test kits. Scanning electron microscopy and X-ray spectra analysis of osmium tetroxide-stained coupons demonstrated the development of microbial biofilm communities on some metal coupons submerged for 3 weeks in storage basins. After 12 months, coupons were fully covered by biofilms, with some deterioration of the coupon surface evident at the microscopical level. These results suggest that, despite the oligotrophic and radiological environment of the SRS storage basins and the active water deionization treatments commonly applied to prevent electrochemical corrosion in these facilities, these conditions do not prevent microbial colonization and survival. Such microbial densities and wide diversity of carbon source utilization reflect the ability of the microbial populations to adapt to these environments. The presumptive presence of sulfate-reducing bacteria and acid-producing bacteria and the development of biofilms on submerged coupons indicated that an environment for MIC of metal components in the storage basins may occur. However, to date, there has been no indication or evidence of MIC in the basins. Basin chemistry control and corrosion surveillance programs instituted several years ago have substantially abated all corrosion mechanisms.

Bacteriological Techniques↗

PubMed1979

Qualitative and quantitative aspects of labeling cell surface carbohydrates using lectins as probes.

Lectins are proteins which bind mono- and oligosaccharides with great specificity. Many polysaccharides, glycoproteins and glycolipids which are important constituents of cell walls and surface membranes of prokaryotic and eukaryotic cells, contain sugar moieties with which lectins can interact. As a result lectins have been extensively used for the study of cell surface and membrane structure of their labeling. This paper reviews and evaluates the available methods for the preparation of fluorescent, electron-dense and radioactive lectin derivatives. The procedures involved in the visualization of lectin binding under light and electron microscopy are described. In addition, the methods for quantitative evaluation of the fluorescence on labeled cells and for analysis of the number of cell surface lectin binding sites using radioactively-labeled lectins are outlined. Examples are given for the application of fluorescent lectin derivatives for the detection of specific saccharide-containing molecules on the surfaces of living or fixed microbial cells and various normal and neoplastic cells. The use of lectins to demonstrate the dynamic nature of cell membranes and to detect changes in membrane structure or organization which occur or organization which occur during differentiation, development or after neoplastic transformation is discussed.

Carbohydrates↗

PubMed1979

[Use of a method of staining sections with methyl green-pyronine for histobacterioscopic purposes].

A method of staining of histological sections with methyl green-pyronine for histobacterioscopic detection of microflora in tissues is proposed. A bright red staining with pyronine of microbial agents and yeast-like fungi of the genus Candida due to a high content of RNA in them permits elective detection of their insignificant amounts in tissues even at low magnifications of the microscope.

Bacteriological Techniques↗

PubMed1974

Microbial response to drought in a Texas highplains shortgrass prairie.

The population of the microbial flora of a mixed blue gramma grass (Bouteloua gracilis H. B. K.) and prickly pear (Opuntia polyacantha Haw.) prairie near Amarillo, Texas, was studied during 1971 after a severe drought. Bacteria, fungi, and algae were estimated by plate count and terminal dilution procedures. Rates of grass and paper decomposition were determined. The microbial flora of soil associated with bovine-grazed grass did not differ significantly from the flora associated with ungrazed grass, either qualitatively or quantitatively. During drought, a greater number of fungi were found in soil associated with prickly pear than in that associated with blue gramma grass. The microbial biomass decreased one full log between the surface and a depth of 50 cm, and the percentage of anaerobes increased with depth. The maximum numbers of fungi and algae detected were 8 x 10 and 6 x 10/g respectively. A linear relationship existed between the microbial biomass and soil moisture. The maximum number of aerobic, heterotrophic bacteria detected was 1.5 x 10 viable cells per g of soil.

Journal Article↗

PubMed1999

Development of a polymerase chain reaction-based assay for the detection of Alternaria fungal contamination in food products.

Alternaria sp. are important fungal contaminants of vegetable, fruit, and grain products, including Alternaria alternata, a contaminant of tomato products. To date, the Howard method, based on microscopic observation of fungal filaments, has been the standard examination for inspection of tomato products. We report development of a polymerase chain reaction (PCR)-based method for detection of Alternaria DNA. PCR primers were designed to anneal to the internal transcribed regions ITS1 and ITS2 of the 5.8S rRNA gene of Alternaria but not to other microbial or tomato DNA. We demonstrate use of the PCR assay to detect Alternaria DNA in experimentally infested and commercially obtained tomato sauce and tomato powder. Use of the PCR method offers a rapid and sensitive assay for the presence of Alternaria DNA in tomato products. The apparent breakdown of DNA in tomato sauce may limit the utility of the assay to freshly prepared products. The assay for tomato powder is not affected by storage time.

Alternaria↗

PubMed2003

Molecular assays for detection of human metapneumovirus.

The recent description of the respiratory pathogen human metapneumovirus (hMPV) has highlighted a deficiency in current diagnostic techniques for viral agents associated with acute lower respiratory tract infections. We describe two novel approaches to the detection of viral RNA by use of reverse transcriptase PCR (RT-PCR). The PCR products were identified after capture onto a solid-phase medium by hybridization with a sequence-specific, biotinylated oligonucleotide probe. The assay was applied to the screening of 329 nasopharyngeal aspirates sampled from patients suffering from respiratory tract disease. These samples were negative for other common microbial causes of respiratory tract disease. We were able to detect hMPV sequences in 32 (9.7%) samples collected from Australian patients during 2001. To further reduce result turnaround times we designed a fluorogenic TaqMan oligoprobe and combined it with the existing primers for use on the LightCycler platform. The real-time RT-PCR proved to be highly reproducible and detected hMPV in an additional 6 out of 62 samples (9.6%) tested during the comparison of the two diagnostic approaches. We found the real-time RT-PCR to be the test of choice for future investigation of samples for hMPV due to its speed, reproducibility, specificity, and sensitivity.

DNA Primers↗

PubMed2003

Bromate induces loss of heterozygosity in the thymidine kinase gene of L5178Y/Tk(+/-)-3.7.2C mouse lymphoma cells.

Potassium bromate (KBrO(3)) induces DNA damage and tumors in mice and rats, but is a relatively weak mutagen in microbial assays and the in vitro mammalian Hprt assay. Concern that there may be a human health risk associated with bromate, a disinfectant by-product of ozonation, has accompanied the increasing use of ozonation as an alternative to chlorination for treatment of drinking water. In this study, we have evaluated the mutagenicity of KBrO(3) and sodium bromate (NaBrO(3)) in the Tk gene of mouse lymphoma cells. In contrast to the weak mutagenic activity seen in the previous studies, bromate induced a mutant frequency of over 100 x 10(-6) at 0.6mM with minimal cytotoxicity (70-80% survival) and over 1300 x 10(-6) at 3mM ( approximately 10% survival). The increase in the Tk mutant frequency was primarily due to the induction of small colony of Tk mutants. Loss of heterozygosity (LOH) analysis of 384 mutants from control and 2.7 mM KBrO(3)-treated cells showed that almost all (99%) bromate-induced mutants resulted from LOH, whereas in the control cultures 77% of the Tk mutants were LOH. Our results suggest that bromate is a potent mutagen in the Tk gene of mouse lymphoma cells, and the mechanism of action primarily involves LOH. The ability of the mouse lymphoma assay to detect a wider array of mutational events than the microbial or V79 Hprt assays may account for the potent mutagenic response.

Animals↗

PubMedDate not supplied

Nonsevere community-acquired pneumonia: correlation between cause and severity or comorbidity.

BACKGROUND: Community-acquired pneumonia frequently constitutes a nonsevere infection manageable at home. However, for these low-risk episodes, the epidemiological features have not been carefully analyzed. OBJECTIVES: To determine the cause of nonsevere community-acquired pneumonia and to investigate if a correlation exists between cause and severity or comorbidity. METHODS: During a 3-year period, all patients with nonsevere community-acquired pneumonia, according to the Pneumonia Patient Outcome Research Team prognostic classification (patients in groups 1-3), were included in the study. Causes were investigated through the following procedures: cultures of blood, sputum, and pleural fluid; serologic tests; and polymerase chain reaction methods to detect Streptococcus pneumoniae DNA in whole blood or Mycoplasma pneumoniae and Chlamydia pneumoniae DNA in throat swab specimens. RESULTS: Of 317 initially included patients, 247 were eligible for the study. A microbial diagnosis was obtained in 162 patients (66%), and the main pathogens detected were S pneumoniae (69 patients [28%]), M pneumoniae (40 patients [16%]), and C pneumoniae (28 patients [11%]). For the 58 patients in prognostic group 1, M pneumoniae was the most prevalent cause, and atypical microorganisms constituted 40 (69%) of the isolated agents. In contrast, for patients in prognostic groups 2 and 3, S pneumoniae was the leading agent, and a significant reduction of M pneumoniae cases and a greater presence of other more uncommon pathogens were observed. The existence of comorbid conditions was not a determining factor for particular causes. CONCLUSIONS: Among low-risk patients with community-acquired pneumonia, there was a certain correlation between severity and cause. In contrast, the existence of a comorbidity did not have a predictive causative value.

Adult↗

PubMed1993

A novel antimicrobial central venous catheter impregnated with benzalkonium chloride.

Catheter-related sepsis is a common complication associated with the use of central venous catheters (CVC). In an attempt to overcome this problem benzalkonium chloride was incorporated into a CVC polymer. The effect of the presence of benzalkonium chloride on microbial colonization of the CVC was then assessed in vitro. MICs and MBCs of benzalkonium chloride for a range of organisms were performed and good activity against Gram-positive organisms was confirmed. In order to assess the antimicrobial activity of the benzalkonium-chloride-impregnated catheter, 2 cm lengths were placed on to nutrient agar plates inoculated with various micro-organisms. Zones of inhibition against five strains of Staphylococcus epidermidis and two strains of Staphylococcus aureus were demonstrated. Smaller zones of inhibition was also produced with Gram-negative species and Candida albicans. The zone sizes correlated with the MICs. Bacterial adherence to the benzalkonium-chloride-impregnated catheters was determined in both static and dynamic models and was significantly reduced compared with control catheters, containing no antimicrobial agent (P < 0.01). Inhibition of microbial adherence to benzalkonium-chloride-impregnated catheters placed in 25% human blood in phosphate-buffered saline (PBS), for up to seven days or PBS alone for 14 days was detected. The findings indicate that benzalkonium-chloride-impregnated catheters exhibit reduced microbial colonization by a range of organisms in vitro. The incorporation of benzalkonium chloride into a CVC may thus offer an effective method for the prevention of catheter related sepsis.

Bacteria↗